ID code: 438D, AR0011 *********************************** ************** ****** CURVES 5.3 R.L. 1998 ***** * 17 May 24 * *********************************** ************** FILE : duplex.pdb lis : dna : axin : axout: daf : pdb : acc : 0.000 wid : 0.750 maxn : 500 ior : 0 ibond: 0 splin: 3 break: -1 NLEVE: 0 NBAC : 7 ends : F supp : T COMB : T dinu : F mini : T rest : F LINE : F zaxe : F FIT : T test : F GRV : F old : T axonl: F Least squares fitting of standard bases ... Str Pos Base Rms (ang) 1 : 1) GA 1 0.031 1 : 2) GA 2 0.026 1 : 3) GA 3 0.052 1 : 4) CA 4 0.014 1 : 5) GA 5 0.039 1 : 6) CA 6 0.025 1 : 7) UA 7 0.021 1 : 8) CA 8 0.025 2 : 1) CB 17 0.033 2 : 2) UB 16 0.023 2 : 3) CB 15 0.049 2 : 4) GB 14 0.028 2 : 5) CB 13 0.018 2 : 6) GB 12 0.026 2 : 7) GB 11 0.025 2 : 8) GB 10 0.034 Strand= 2 Nucleo= 16 Atoms = 338 Units = 16 Input 1) Xdisp= 0.00 Ydisp= 0.00 Inclin= 0.00 Tip= 0.00 Combined strands have 8 levels ... Strand 1 has 8 bases (5'-3'): GGGCGCUC Strand 2 has 8 bases (3'-5'): CUCGCGGG FIRST SUM= 96.657 CPTS: 1.648 20.676 7.134 67.199 MINIMISATION: ACC = 0.100E-05 MAXN= 500 NVAR= 32 STEP 1 SUM= 96.657 DEL= 0.000E+00 STEP 2 SUM= 75.084 DEL= -0.216E+02 STEP 3 SUM= 54.339 DEL= -0.207E+02 STEP 4 SUM= 42.280 DEL= -0.121E+02 STEP 5 SUM= 37.519 DEL= -0.476E+01 STEP 6 SUM= 31.551 DEL= -0.597E+01 STEP 7 SUM= 32.630 DEL= 0.108E+01 STEP 8 SUM= 28.814 DEL= -0.382E+01 STEP 9 SUM= 25.761 DEL= -0.305E+01 STEP 10 SUM= 21.891 DEL= -0.387E+01 STEP 11 SUM= 21.469 DEL= -0.423E+00 STEP 12 SUM= 19.844 DEL= -0.162E+01 STEP 13 SUM= 34.822 DEL= 0.150E+02 STEP 14 SUM= 19.624 DEL= -0.152E+02 STEP 15 SUM= 19.228 DEL= -0.396E+00 STEP 16 SUM= 18.503 DEL= -0.724E+00 STEP 17 SUM= 25.196 DEL= 0.669E+01 STEP 18 SUM= 18.363 DEL= -0.683E+01 STEP 19 SUM= 18.268 DEL= -0.946E-01 STEP 20 SUM= 18.196 DEL= -0.721E-01 STEP 21 SUM= 18.082 DEL= -0.114E+00 STEP 22 SUM= 17.983 DEL= -0.997E-01 STEP 23 SUM= 17.798 DEL= -0.185E+00 STEP 24 SUM= 17.299 DEL= -0.499E+00 STEP 25 SUM= 17.035 DEL= -0.264E+00 STEP 26 SUM= 16.674 DEL= -0.361E+00 STEP 27 SUM= 16.522 DEL= -0.152E+00 STEP 28 SUM= 16.322 DEL= -0.201E+00 STEP 29 SUM= 16.203 DEL= -0.118E+00 STEP 30 SUM= 16.100 DEL= -0.104E+00 STEP 31 SUM= 16.050 DEL= -0.497E-01 STEP 32 SUM= 16.033 DEL= -0.172E-01 STEP 33 SUM= 16.029 DEL= -0.418E-02 STEP 34 SUM= 16.028 DEL= -0.119E-02 STEP 35 SUM= 16.027 DEL= -0.206E-03 STEP 36 SUM= 16.027 DEL= -0.171E-03 STEP 37 SUM= 16.027 DEL= -0.178E-03 STEP 38 SUM= 16.027 DEL= -0.577E-04 STEP 39 SUM= 16.027 DEL= -0.454E-04 STEP 40 SUM= 16.027 DEL= -0.402E-04 STEP 41 SUM= 16.027 DEL= -0.265E-04 STEP 42 SUM= 16.027 DEL= -0.200E-04 STEP 43 SUM= 16.027 DEL= -0.395E-05 STEP 44 SUM= 16.027 DEL= -0.342E-06 STEP 45 SUM= 16.027 DEL= -0.373E-07 STEP 46 SUM= 16.027 DEL= -0.107E-08 STEP 47 SUM= 16.027 DEL= -0.124E-10 STEP 48 SUM= 16.027 DEL= -0.139E-11 STEP 49 SUM= 16.027 DEL= 0.000E+00 STEP 50 SUM= 16.027 DEL= 0.000E+00 STEP 51 SUM= 16.027 DEL= -0.355E-14 STEP 52 SUM= 16.027 DEL= 0.000E+00 FINAL SUM= 16.027 CPTS: 1.024 12.461 1.085 1.456 GRA= 0.10E-09-0.20E-08-0.28E-10-0.14E-09-0.19E-09 0.29E-08 0.23E-10 0.28E-09 GRA=-0.44E-09-0.47E-08 0.38E-10-0.39E-09-0.86E-11 0.49E-08-0.21E-09 0.40E-09 GRA=-0.51E-09-0.16E-08 0.10E-09-0.89E-10-0.51E-10 0.11E-08 0.84E-10 0.70E-10 GRA=-0.11E-09-0.12E-08-0.24E-09-0.79E-10 0.38E-09 0.92E-09 0.11E-09 0.73E-10 ---------------------------- |A| Global axis parameters | ---------------------------- 1) U: -0.134 0.017 0.991 P: 34.788 11.626 -10.077 D: 3.152 2) U: -0.073 0.016 0.997 P: 34.120 11.446 -7.588 D: 3.752 3) U: -0.016 0.071 0.997 P: 34.072 11.920 -4.895 D: 1.138 4) U: 0.113 0.004 0.994 P: 34.119 11.888 -2.334 D: 1.132 5) U: 0.203 0.056 0.978 P: 34.900 12.049 0.418 D: 0.547 6) U: 0.195 0.013 0.981 P: 35.646 11.860 3.523 D: 2.825 7) U: 0.233 0.019 0.972 P: 36.009 11.742 6.454 D: 3.480 8) U: 0.309 0.065 0.949 P: 36.767 12.042 9.024 --------------------------------- |B| Global Base-Axis Parameters | --------------------------------- 1st strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) GA 1 -4.31 0.19 12.85 -7.06 1 0 2) GA 2 -5.23 -0.33 13.86 -9.13 1 1 3) GA 3 -4.08 0.40 13.59 -8.66 1 5 4) CA 4 -4.38 0.04 16.16 -8.79 3 -13 5) GA 5 -4.02 -0.13 6.77 -5.94 1 13 6) CA 6 -3.90 -0.46 5.50 -4.84 3 -7 7) UA 7 -2.83 -0.32 8.29 -9.15 4 -17 8) CA 8 -3.87 -0.13 17.05 -6.42 3 0 2nd strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) CB 17 -4.15 -0.36 10.00 -4.11 3 0 2) UB 16 -3.04 -0.01 8.60 -8.32 4 -17 3) CB 15 -4.19 0.14 6.33 -6.22 3 -7 4) GB 14 -4.22 0.05 10.37 -8.73 1 13 5) CB 13 -3.97 0.23 14.71 -10.99 3 -13 6) GB 12 -4.37 0.11 14.21 -9.49 1 5 7) GB 11 -5.41 -0.25 12.23 -11.43 1 1 8) GB 10 -4.28 0.26 8.10 -7.60 1 0 -------------------------------------- |C| Global Base pair-Axis Parameters | -------------------------------------- Strand 1 with strand 2 ... Duplex Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) G 1-C 17 -4.23 0.28 11.42 -1.47 1 0 2) G 2-U 16 -4.14 -0.16 11.23 -0.40 1 1 3) G 3-C 15 -4.14 0.13 9.96 -1.22 1 5 4) C 4-G 14 -4.30 -0.00 13.27 -0.03 3 -13 5) G 5-C 13 -3.99 -0.18 10.74 2.52 1 13 6) C 6-G 12 -4.13 -0.29 9.85 2.32 3 -7 7) U 7-G 11 -4.12 -0.03 10.26 1.14 4 -17 8) C 8-G 10 -4.08 -0.20 12.57 0.59 3 0 Average: -4.14 -0.06 11.16 0.43 --------------------------------- |D| Global Base-Base Parameters | --------------------------------- Strand 1 with strand 2 ... Duplex Shear Stretch Stagger Buckle Propel Opening Bc Tc (Sx) (Sy) (Sz) (kappa) (omega) (sigma) 1) G 1-C 17 -0.17 -0.17 0.17 2.85 -11.17 1.43 1 0 2) G 2-U 16 -2.20 -0.34 0.11 5.26 -17.45 1.21 1 1 3) G 3-C 15 0.12 0.53 0.65 7.26 -14.88 7.03 1 5 4) C 4-G 14 -0.16 0.09 -0.34 5.79 -17.52 0.78 3 -13 5) G 5-C 13 -0.05 0.10 -0.07 -7.94 -16.93 2.58 1 13 6) C 6-G 12 0.46 -0.35 -0.00 -8.71 -14.32 -0.06 3 -7 7) U 7-G 11 2.58 -0.57 -0.08 -3.94 -20.58 1.64 4 -17 8) C 8-G 10 0.41 0.13 -0.14 8.95 -14.02 1.17 3 0 Average: 0.12 -0.07 0.04 1.19 -15.86 1.97 ---------------------------------- |E| Global Inter-Base Parameters | ---------------------------------- 1st strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 1/G 2 -0.92 -0.99 2.51 -2.05 -0.34 26.75 1 3) G 2/G 3 1.06 1.08 2.98 -4.54 2.04 46.54 1 4) G 3/C 4 -0.40 -0.47 2.07 7.83 6.37 28.26 5 5) C 4/G 5 0.65 -0.35 2.99 -7.87 8.70 35.48 8 6) G 5/C 6 -0.15 -0.50 3.22 -1.27 -1.37 32.12 5 7) C 6/U 7 1.04 0.46 2.90 4.97 -4.95 41.75 -3 8) U 7/C 8 -0.98 0.01 2.66 13.35 0.17 27.17 -2 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) C 17/U 16 1.11 0.81 2.57 -4.47 -5.94 26.97 -2 3) U 16/C 15 -1.25 -0.21 2.44 -6.53 0.53 40.72 -3 4) C 15/G 14 -0.12 0.02 3.06 9.29 -9.01 34.51 5 5) G 14/C 13 0.54 0.36 2.71 5.85 -8.10 33.68 8 6) C 13/G 12 -0.67 0.05 3.15 -0.49 3.98 34.76 5 7) G 12/G 11 -1.08 -0.68 2.98 0.20 -1.31 40.04 1 8) G 11/G 10 1.19 0.69 2.72 0.45 6.39 27.65 1 --------------------------------------- |F| Global Inter-Base pair Parameters | --------------------------------------- Strand 1 with strand 2 ... Duplex Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 1/G 2 0.09 -0.90 2.54 -3.26 2.80 26.86 1 3) G 2/G 3 -0.09 0.64 2.71 -5.54 0.76 43.63 1 4) G 3/C 4 -0.26 -0.25 2.56 8.56 7.69 31.38 5 5) C 4/G 5 0.60 -0.36 2.85 -1.01 8.40 34.58 8 6) G 5/C 6 -0.41 -0.27 3.18 -0.88 -2.67 33.44 5 7) C 6/U 7 -0.02 0.57 2.94 2.59 -1.82 40.89 -3 8) U 7/C 8 0.11 -0.34 2.69 6.90 -3.11 27.41 -2 Average: 0.00 -0.13 2.78 1.05 1.72 34.03 --------------------------------- |G| Local Inter-Base Parameters | --------------------------------- 1st strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 1/G 2 -0.41 -2.48 3.41 1.54 5.82 25.66 1 3) G 2/G 3 1.48 -1.90 3.44 2.36 12.86 45.15 1 4) G 3/C 4 -0.06 -1.81 3.16 11.87 13.11 24.31 5 5) C 4/G 5 1.21 -2.23 3.76 -3.09 15.38 34.52 8 6) G 5/C 6 0.31 -2.36 3.29 1.75 1.98 32.18 5 7) C 6/U 7 1.57 -1.57 2.94 9.70 0.22 40.71 -3 8) U 7/C 8 -0.52 -1.01 2.86 16.65 5.92 25.30 -2 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) C 17/U 16 0.69 -2.06 3.10 -7.31 10.07 25.82 -2 3) U 16/C 15 -1.46 -1.97 2.69 -11.40 4.60 39.16 -3 4) C 15/G 14 -0.60 -2.03 3.80 4.61 13.94 34.23 5 5) G 14/C 13 -0.02 -2.03 3.68 0.17 15.12 32.28 8 6) C 13/G 12 -1.13 -1.75 3.37 -6.45 4.71 33.70 5 7) G 12/G 11 -1.62 -2.02 3.21 -6.69 10.19 38.70 1 8) G 11/G 10 0.69 -2.49 3.17 -3.93 -1.36 27.37 1 -------------------------------------- |H| Local Inter-Base pair Parameters | -------------------------------------- Strand 1 with strand 2 ... Duplex Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 1/G 2 0.13 -2.28 3.16 -2.87 8.00 25.82 1 3) G 2/G 3 -0.02 -1.90 3.22 -4.73 8.94 42.63 1 4) G 3/C 4 -0.27 -1.88 3.49 8.33 13.73 29.48 5 5) C 4/G 5 0.58 -2.12 3.77 -1.48 15.23 33.77 8 6) G 5/C 6 -0.42 -2.04 3.41 -2.36 3.41 33.24 5 7) C 6/U 7 -0.02 -1.79 3.24 1.57 5.25 40.27 -3 8) U 7/C 8 0.10 -1.76 2.91 6.35 2.45 26.59 -2 Average: 0.01 -1.97 3.32 0.69 8.14 33.11 --------------------------- |I| Global Axis Curvature | --------------------------- Duplex Ax Ay Ainc Atip Adis Angle Path Dc 2) G 1/G 2 -0.00 -0.46 -3.07 1.73 0.46 3.52 2.58 1 3) G 2/G 3 -0.09 0.35 -4.27 1.58 0.36 4.55 2.73 1 4) G 3/C 4 -0.10 -0.11 5.25 6.50 0.15 8.35 2.56 5 5) C 4/G 5 0.29 -0.18 1.52 5.84 0.34 6.04 2.87 8 6) G 5/C 6 -0.27 -0.17 0.01 -2.48 0.32 2.48 3.20 5 7) C 6/U 7 -0.03 0.32 2.18 -0.64 0.32 2.27 2.96 -3 8) U 7/C 8 0.07 -0.18 4.59 -2.56 0.19 5.26 2.70 -2 Overall axis bend ... UU= 25.90 PP= 33.09 Duplex Offset L.Dir ... wrt end-to-end vector 1) G 1 0.00 0.00 2) G 2 0.95 61.29 3) G 3 1.26 -7.49 4) C 4 1.47 -31.06 5) G 5 0.99 -74.13 6) C 6 0.55 -88.48 7) U 7 0.55 -110.35 8) C 8 0.00 0.00 Path length= 19.60 End-to-end= 19.21 Shortening= 1.98 % ------------------------- |J| Backbone Parameters | ------------------------- 1st strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)GA 1 -29.59 41.97 11.71 43.47 C3'-endo 106.2 100.5 101.3 2)GA 2 -27.98 44.05 18.38 47.02 C3'-endo 105.5 100.9 99.6 3)GA 3 -29.52 40.15 9.84 41.65 C3'-endo 106.0 101.1 101.2 4)CA 4 -23.49 40.48 23.20 44.65 C3'-endo 106.2 101.4 100.5 5)GA 5 -35.94 40.60 355.09 41.72 C2'-exo 106.0 99.9 102.2 6)CA 6 -26.32 39.93 15.95 42.04 C3'-endo 106.5 101.1 101.9 7)UA 7 -26.39 39.50 15.42 41.67 C3'-endo 106.9 100.9 101.8 8)CA 8 -28.87 42.50 14.57 44.65 C3'-endo 105.9 100.8 100.5 Torsions Chi Gamma Delta Epsil Zeta Alpha Beta C1'-N C5'-C4' C4'-C3' C3'-O3' O3'-P P-O5' O5'-C5' 1)GA 1 -169.39 64.23 83.86 -149.87 -74.36 -66.91 178.10 2)GA 2 -166.95 52.81 82.11 -146.86 -73.80 -60.52 177.99 3)GA 3 -159.19 45.18 86.88 -143.64 -74.67 -60.14 172.14 4)CA 4 -148.29 45.11 77.56 -176.15 -56.70 151.31 170.54 5)GA 5 -172.70 -176.74 90.35 -138.81 -67.43 -61.64 170.57 6)CA 6 -167.21 54.48 82.68 -145.18 -70.96 -65.58 164.54 7)UA 7 -160.10 62.31 83.92 -144.35 -81.47 -75.60 167.42 8)CA 8 -147.45 60.69 78.41 ...... ...... ...... ...... 2nd strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)CB 17 -23.85 39.45 21.36 43.07 C3'-endo 106.5 101.4 100.7 2)UB 16 -26.11 40.00 16.81 42.42 C3'-endo 106.6 101.2 101.5 3)CB 15 -25.31 38.56 16.83 41.01 C3'-endo 107.0 101.6 101.3 4)GB 14 -33.49 42.13 4.57 43.30 C3'-endo 105.9 100.6 100.3 5)CB 13 -30.20 44.96 15.01 47.18 C3'-endo 105.8 100.1 99.9 6)GB 12 -28.16 43.00 16.70 45.58 C3'-endo 106.4 100.4 100.3 7)GB 11 -27.26 41.45 16.28 43.87 C3'-endo 106.4 100.5 101.3 8)GB 10 -35.23 43.76 2.31 44.56 C3'-endo 105.7 99.6 101.3 Torsions Chi Gamma Delta Epsil Zeta Alpha Beta C1'-N C5'-C4' C4'-C3' C3'-O3' O3'-P P-O5' O5'-C5' 1)CB 17 -156.75 59.66 80.52 ...... ...... ...... ...... 2)UB 16 -162.14 51.89 83.50 -158.66 -71.20 -77.85 -176.25 3)CB 15 -171.64 48.56 82.74 -143.24 -74.66 -58.06 163.42 4)GB 14 -162.70 50.77 82.58 -139.58 -78.20 -60.80 166.04 5)CB 13 -159.02 52.50 79.50 -155.68 -70.89 -66.87 -177.01 6)GB 12 -159.56 54.55 79.18 -147.67 -73.14 -60.77 171.01 7)GB 11 -162.93 50.50 82.22 -147.54 -63.47 -68.37 177.13 8)GB 10 -175.14 69.50 88.63 -147.10 -71.53 -66.30 -178.65